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- PDB-4hda: Crystal structure of human Sirt5 in complex with Fluor-de-Lys pep... -

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Basic information

Entry
Database: PDB / ID: 4hda
TitleCrystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol
Components
  • Fluor-de-Lys peptide
  • NAD-dependent protein deacylase sirtuin-5, mitochondrial
KeywordsHYDROLASE/HYDROLASE ACTIVATOR / NAD-dependent deacetylase / Sirtuin / mitochondrial / activator complex / resveratrol / HYDROLASE-HYDROLASE ACTIVATOR complex
Function / homology
Function and homology information


protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity ...protein demalonylation / protein deglutarylation / regulation of ketone biosynthetic process / peptidyl-lysine demalonylation / protein desuccinylation / peptidyl-lysine desuccinylation / protein-glutaryllysine deglutarylase activity / protein-malonyllysine demalonylase activity / protein-succinyllysine desuccinylase activity / NAD-dependent protein lysine deacetylase activity / protein deacetylation / negative regulation of cardiac muscle cell apoptotic process / NAD+ binding / negative regulation of reactive oxygen species metabolic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / epigenetic regulation of gene expression / response to nutrient levels / mitochondrion organization / Transcriptional activation of mitochondrial biogenesis / mitochondrial intermembrane space / transferase activity / mitochondrial matrix / mitochondrion / zinc ion binding / nucleus / cytosol
Similarity search - Function
Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain ...Sirtuin, class III / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
RESVERATROL / NAD-dependent protein deacylase sirtuin-5, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsGertz, M. / Steegborn, C.
CitationJournal: Plos One / Year: 2012
Title: A molecular mechanism for direct sirtuin activation by resveratrol.
Authors: Gertz, M. / Nguyen, G.T. / Fischer, F. / Suenkel, B. / Schlicker, C. / Franzel, B. / Tomaschewski, J. / Aladini, F. / Becker, C. / Wolters, D. / Steegborn, C.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
F: Fluor-de-Lys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9556
Polymers60,5963
Non-polymers3593
Water27015
1
A: NAD-dependent protein deacylase sirtuin-5, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9782
Polymers29,9131
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent protein deacylase sirtuin-5, mitochondrial
F: Fluor-de-Lys peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9774
Polymers30,6832
Non-polymers2942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.300, 112.690, 55.890
Angle α, β, γ (deg.)90.00, 90.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacylase sirtuin-5, mitochondrial / Regulatory protein SIR2 homolog 5 / SIR2-like protein 5


Mass: 29913.078 Da / Num. of mol.: 2 / Fragment: UNP residues 34-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIR2L5, SIRT5 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta2
References: UniProt: Q9NXA8, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide Fluor-de-Lys peptide


Mass: 769.913 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: coumarin-modified tetra peptide
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 150 mM NH4Cl, 15% (w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.521
ReflectionResolution: 2.6→38.8 Å / Num. all: 15731 / Num. obs: 15354 / % possible obs: 97.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.5
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3 / % possible all: 93.4

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→38.778 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8104 / σ(F): 0 / Phase error: 25.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 776 5.05 %using phenix and taking the twin operation into account
Rwork0.1986 14570 --
obs0.2046 15353 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.671 Å2 / ksol: 0.334 e/Å3
Displacement parametersBiso max: 102.99 Å2 / Biso mean: 40.8352 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1-5.02 Å2-0 Å2-4.0806 Å2
2--11.9911 Å2-0 Å2
3----17.0111 Å2
Refinement stepCycle: LAST / Resolution: 2.601→38.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4155 0 19 15 4189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074289
X-RAY DIFFRACTIONf_angle_d1.3255821
X-RAY DIFFRACTIONf_dihedral_angle_d19.9591567
X-RAY DIFFRACTIONf_chiral_restr0.069621
X-RAY DIFFRACTIONf_plane_restr0.008767
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.6058-2.80690.37821510.32182834283491
2.8069-3.0890.32811510.25052882288293
3.089-3.53520.25441540.20552915291593
3.5352-4.45110.2271540.17712948294894
4.4511-27.94660.21521500.16892991299194

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